Not sure if this falls into your area or not; but some of the effects that can be applied are destructive. For instance limiting. The Adaptive Limiter changes not only the dynamic; but also the length. Whereas the Limiter does not. Whether the process you use changes the file length or not is easily recognized by the check box on the right side of the Actions List. If it's "red", the effect has changed the length, and thus, put the track out of sync.
Excerpt from the manual.
Limitations of Actions That Change the File?s Length
Some actions change the overall length of the audio file by inserting or deleting audio. These include inserting silence, noise, or a waveform, time stretching, and deleting part of a file. Recording audio, pasting, and adding an effect with a ?tail? can also change the file?s length. In the Actions list, the selection checkbox for each action that changes the file?s length appears red, making it easy to visually distinguish those actions.